Identification of three new alternate human kallikrein 2 transcripts: evidence of long transcript and alternative splicing

Arthropod venoms: Biochemistry, ecology and evolution

Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.

Discovery of novel transcripts of the human tissue kallikrein (KLK1) and kallikrein-related peptidase 2 (KLK2) in human cancer cells, exploiting Next-Generation Sequencing technology

Tissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional properties. Several KLK transcripts have been found aberrantly expressed in numerous human malignancies, confirming their prognostic or/and diagnostic values. However, the process of alternative splicing can now be studied in-depth due to the development of Next-Generation Sequencing (NGS). In the present study, we used NGS to discover novel transcripts of the KLK1 and KLK2 genes, after nested touchdown PCR. Bioinformatics analysis and PCR experiments revealed a total of eleven novel KLK transcripts (two KLK1 and nine KLK2 transcripts). In addition, the expression profiles of each novel transcript were investigated with nested PCR experiments using variant-specific primers. Since KLKs are implicated in human malignancies, qualifying as potential biomarkers, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer.

The Tissue Kallikrein Family of Serine Proteases: Functional Roles in Human Disease and Potential as Clinical Biomarkers

Prostate specific antigen (PSA) or human kallikrein 3 (hK3) has long been an effective biomarker for prostate cancer. Now, other members of the tissue kallikrein (KLK) gene family are fast becoming of clinical interest due to their potential as prognostic biomarkers. particularly for hormone dependent cancers. The tissue kallikreins are serine proteases that are encoded by highly conserved multi-gene family clusters in rodents and humans. The rat and mouse loci contain 10 and 25 functional genes, respectively, while the human locus at 19q 13.4 contains 15 genes. The structural organization and size of these genes are similar across species; all genes have 5 coding exons that encode a prepro-enzyme. Although the physiological activators of these zymogens have not been described, in vitro biochemical studies show that some kallikreins can auto-activate and others can activate each other, suggesting that the kallikreins may participate in an enzymatic cascade similar to that of the coagulation cascade. These genes are expressed, to varying degrees, in a wide range of tissues suggesting a functional involvement in a diverse range of physiological and pathophysiological processes. These include roles in normal skin desquamation and psoriatic lesions, tooth development, neural plasticity, and Alzheimer's disease (AD). Of particular interest is the expression of many kallikreins in prostate, ovarian, and breast cancers where they are emerging as useful prognostic indicators of disease progression.

Human tissue kallikreins: A road under construction

BACKGROUND

The human tissue kallikrein gene family, located at chromosome 19q13.4, is the largest contiguous family of proteases in the human genome. The locus encodes all 15 members of the family, 13 of which have been reported as potential biomarkers for several carcinomas and other non-neoplastic diseases. Kallikreins are expressed by a wide range of tissues and implicated in a number of physiological functions, including skin desquamation, semen liquefaction, neural plasticity and the regulation of blood pressure. Kallikrein function is regulated at various levels, including transcription, translation and post-translation. The proteolytic activity of kallikreins is believed to be cascade mediated and may cross-talk with other proteases. These cascades are highly regulated through a series of feedback loops, inhibitors, (auto) degradation and internal cleavage. Uncontrolled proteolytic activity of kallikreins is implicated in a large number of neoplastic and non-neoplastic pathological conditions.

CONCLUSIONS

As our understanding of their regulatory and functional mechanisms continues to expand, kallikreins are expected to become novel targets for the design of new therapeutics.

Kallikrein-related peptidase (KLK) family mRNA variants and protein isoforms in hormone-related cancers: do they have a function?

The kallikrein-related peptidase (KLK) gene family of 15 serine proteases encodes many proteins, including prostate specific antigen (PSA or KLK3), that are well described and/or are potential biomarkers for hormone-related cancers. Variant mRNA transcripts produced by alternative splicing, polyadenylation or AUG sites, or intron retention have been found for each of the KLK genes. The predicted protein for many of these alternative transcripts is different from that of the classical kallikrein-related peptidases and would not be an active serine protease. The majority of these novel protein isoforms have not been studied in vivo. The possible function(s) of the variant transcripts/protein isoforms and potential roles that they may play in hormone-related cancers are still unknown and are the focus of this short review.

A survey of alternative transcripts of human tissue kallikrein genes

Alternative splicing is prevalent within the human tissue kallikrein gene locus. Aside from being the most important source of protein diversity in eukaryotes, this process plays a significant role in development, physiology and disease. A better understanding of alternative splicing could lead to the use of gene variants as drug targets, therapeutic agents or diagnostic markers. With the rapidly rising number of alternative kallikrein transcripts, classifying new transcripts and piecing together the significance of existing data are becoming increasingly challenging. In this review, we present a systematic analysis of all currently known kallikrein alternative transcripts. By defining a reference form for each of the 15 kallikrein genes (KLK1 to KLK15), we were able to classify alternative splicing patterns. We identified 82 different kallikrein gene transcript forms, including reference forms. Alternative splicing may lead to the synthesis of 56 different protein forms for KLK1-15. In the kallikrein locus, the majority of alternative splicing events occur within the protein-coding region, and to a lesser extent in the 5' untranslated regions (UTRs). The most common alternative splicing event is exon skipping (35%) and the least common events are cryptic exons (3%) and internal exon deletion (3%). Seventy-six percent of kallikrein splice variants that are predicted to encode truncated proteins are the result of frameshifts. Eighty-nine percent of putative proteins encoded by splice variants are predicted to be secreted. Although several reports describe the identification of kallikrein splice variants and their potential clinical utility, this is the first extensive review on this subject. Accumulating evidence suggests that alternative kallikrein forms could be involved in many pathologic conditions or could have practical applications as biomarkers. The organization and analysis of the kallikrein transcripts will facilitate future work in this area and may lead to novel clinical and diagnostic applications.

IDENTIFYING THE COMBINATION OF THE TRANSCRIPTIONAL REGULATORY SEQUENCES ON PROSTATE SPECIFIC ANTIGEN AND HUMAN GLANDULAR KALLIKREIN GENES

PURPOSE

The combination of prostate specific antigen (PSA) and human glandular kallikrein (KLK2) promoters and/or enhancers was used to establish a new model to determine the feasibility of tissue specific expression for prostate cancer.

MATERIALS AND METHODS

In vitro studies used the construction of PSA and KLK2 promoters/enhancers vectors to elucidate the link between the promoter/enhancer of PSA and KLK2. Reverse transcriptase-polymerase chain reaction assays were used to determine cell specific expression. Therefore, an attractive tissue specific expression vector for PSA and KLK2 gene was identified.

RESULTS

The reporter vectors driven by KLK2 promoter had much lower luciferase activities than those of the reporter vectors driven by PSA promoter in LNCaP cells. Furthermore, the most efficient and cell specific reporter activity after 5alpha-androstan-17beta-ol-3-one treatment among the reporter vectors constructed in this study was that of pKLK2EPSABHE, which was driven by KLK2 enhancer and PSA promoter/enhancer. The pKLK2EPSABHE reporter vector could induce 800-fold higher than the KLK2 basic promoter and its reporter activity was 16 times that of the enhancer/promoter element of KLK2 following induction by androgen.

CONCLUSIONS

The results verify that the PSA promoter/enhancer must be combined with KLK2 to ensure the full activity and cell specificity of the gene. These expressions coupled with mechanic target validation yield valuable clues regarding the model of action of complex mixtures. This model is a potentially useful tool in gene therapy for metastatic prostate cancer.

Cloning and characterization of novel isoforms of the human kallikrein 6 gene

Human kallikrein 6 (protease M/zyme/neurosin) was originally identified based on its aberrant expression in tumor cells and is considered a biomarker for ovarian cancer. Here, we describe the identification, cloning, and tissue expression of three novel transcript variants of the KLK6 gene that encode for wild-type kallikrein 6. Contrary to the classical form, transcript variants contain one untranslated exon, exploit intronic sequences, and are likely products of alternative promoters. In addition, we cloned splice variants 2 and 3 produced by splicing out exons 3 and 4, respectively. Given the potential diagnostic applications of kallikrein 6 at both the mRNA and protein levels, we developed a duplex RT-PCR, in order to differentially detect and quantitate mRNA species corresponding to splice variants. We show that in normal mammary epithelial cells and mammary tumor cell lines that overexpress the KLK6 gene, splice variants account for approximately 10-20% of all mRNA species.

Human Tissue Kallikreins: Physiologic Roles and Applications in Cancer

Tissue kallikreins are members of the S1 family (clan SA) of trypsin-like serine proteases and are present in at least six mammalian orders. In humans, tissue kallikreins (hK) are encoded by 15 structurally similar, steroid hormone–regulated genes (KLK) that colocalize to chromosome 19q13.4, representing the largest cluster of contiguous protease genes in the entire genome. hKs are widely expressed in diverse tissues and implicated in a range of normal physiologic functions from the regulation of blood pressure and electrolyte balance to tissue remodeling, prohormone processing, neural plasticity, and skin desquamation. Several lines of evidence suggest that hKs may be involved in cascade reactions and that cross-talk may exist with proteases of other catalytic classes. The proteolytic activity of hKs is regulated in several ways including zymogen activation, endogenous inhibitors, such as serpins, and via internal (auto)cleavage leading to inactivation. Dysregulated hK expression is associated with multiple diseases, primarily cancer. As a consequence, many kallikreins, in addition to hK3/PSA, have been identified as promising diagnostic and/or prognostic biomarkers for several cancer types, including ovarian, breast, and prostate. Recent data also suggest that hKs may be causally involved in carcinogenesis, particularly in tumor metastasis and invasion, and, thus, may represent attractive drug targets to consider for therapeutic intervention.

Quantitative analysis of hippostasin/KLK11 gene expression in cancerous and noncancerous prostatic tissues

OBJECTIVES

Hippostasin/kallikrein 11 (KLK11) is a member of the human kallikrein gene family, which includes prostate-specific antigen (PSA), human kallikrein 2 (hK2), and another 12 members, all localized on chromosome 19q13.4. Hippostasin has two alternative splicing isoforms, known as the brain type and prostate type. We have previously reported that the prostate-type isoform is not expressed in human prostate cancer cell lines.

METHODS

We compared the expression of hippostasin/KLK11 isoforms in 76 matched pairs of human normal and prostate cancer tissues by quantitative reverse transcriptase-polymerase chain reaction.

RESULTS

The expression of both isoforms of KLK11 was 25% to 45% higher in cancer tissues compared with their normal counterparts. Regarding prostate-type KLK11, we identified a significant association between lower expression and higher tumor stage, Gleason score, and tumor grade. No such association was seen with the brain-type isoform.

CONCLUSIONS

: The expression of the prostate-type isoform of KLK11 is increased in prostate cancer. This parameter should be examined further as a new prognostic indicator of prostate cancer.

Molecular cloning and expression of a variant form of hippostasin/KLK11 in prostate

BACKGROUND

Hippostasin is a kallikrein-like serine protease, which has two alternatively spliced isoforms, brain-type and prostate-type. We previously reported alternative expression of hippostasin in prostate cancer cell lines.

METHODS

We studied the expression of a variant-form hippostasin (isoform 3) mRNA by RT-PCR. Localization of the isoform 3 protein was examined by immunohistochemistry. The enzymatic activity of the recombinant protein was measured with synthetic substrates.

RESULTS

A novel isoform of hippostasin contains 25 additional amino acids in the catalytic triad of brain-type hippostasin. Its mRNA was expressed in normal prostate tissue, BPH, and prostate cancer cell lines. The protein was localized in the prostate secretory epithelium. The enzyme activity was similar to that of brain-type hippostasin, which has kallikrein-like activity.

CONCLUSIONS

In this study, we have identified a third isoform of hippostasin, which was designated variant-form (isoform 3). Hippostasin isoform 3 may play a role in the prostate, including reproductive and/or tumorigenic functions.

Increase of functional diversity by alternative splicing

A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by chance, whereas disruption of domains and other structural modules is less frequent. If domain regions are disrupted, the functional effect, as predicted from 3D structure, is frequently equivalent to removal of the entire domain. Also, short alternative splicing events within domains, which might preserve folded structure, target functional residues more frequently than expected. Thus, it seems that positive selection has had a major role in the evolution of alternative splicing.

Unusual alternative splicing within the human kallikrein genes KLK2 and KLK3 gives rise to novel prostate-specific proteins

Prostate-specific antigen (PSA) and human kallikrein 2 are closely related products of the human kallikrein genes KLK3 and KLK2, respectively. Both PSA and human kallikrein 2 are produced and secreted in the prostate and have important applications in the diagnosis of prostate cancer. We report here the identification of unusual mRNA splice variants of the KLK2 and KLK3 genes that result from inclusion of intronic sequences adjacent to the first exon. The novel proteins encoded by these transcripts, named PSA-linked molecule (PSA-LM) and hK2-linked molecule (K-LM), share only the signal peptide with the original protein product of the respective gene. The mature proteins are entirely different and bear no similarity to the kallikrein family or to other proteins in the databases. As is the case with PSA, PSA-LM is expressed in the secretory epithelial cells of the prostate and is up-regulated in response to androgenic stimulation. A similar pattern of expression is suggested for K-LM.

GDEP, a new gene differentially expressed in normal prostate and prostate cancer

BACKGROUND

The database of human expressed sequence tags (dbEST) is a potential source for the identification of tissue specific genes. The database contains sequences that originate from cDNA libraries from different tissues cell types and tumors.

METHODS

Computer based analysis identified a cluster of sequence homologous ESTs, containing ESTs derived only from human prostate cDNA libraries. The tissue specificity was examined by multiple tissue RNA dot blots and RT-PCR. The new RNA transcript was characterized using northern blot analysis, RACE-PCR, and a ribonuclease protection assay.

RESULTS

We have identified a gene differentially expressed in prostate using EST database analysis and experimental studies. We name the gene GDEP for gene differentially expressed in prostate. The major GDEP transcript is about 520 bp long. GDEP RNA was detected in nine prostate tissue samples, four normal and five cancer. Expression in prostate epithelial cells was established by in situ hybridization. Weak expression was detected in the prostate cancer cell line LNCaP. In vitro transcription/translation indicate that the RNA encodes a small 34 amino acid protein. The major transcript consists of two exons with one large intron (> 15 kb). The GDEP gene was mapped to chromosome 4q21.1 by radiation hybrid mapping.

CONCLUSIONS

Our data proves that tissue specific genes can be identified by EST database mining. The prostate specificity of GDEP expression indicates that GDEP may be useful in the diagnosis or treatment of prostate cancer. Published 2001 Wiley-Liss, Inc.

Alternative splicing isoforms of hippostasin (PRSS20/KLK11) in prostate cancer cell lines

BACKGROUND

Hippostasin is a kallikrein-like protease (PRSS20/KLK11), which is expressed preferentially in the hippocampus and prostate. We have reported that alternative splicing variants of human hippostasin are regulated in a tissue-specific manner. Brain-type hippostasin consists of 250 amino acids including a typical signal sequence, and is expressed in the brain and prostate. The prostate-type hippostasin, which has 32 extra amino acids at the N-terminal end, is expressed only in the prostate.

METHODS

We analyzed the expression and localization of hippostasin in normal prostate tissue, BPH tissue, and prostate cancer cell lines. We performed northern blotting, in situ hybridization, immunohistochemistry, and RT-PCR.

RESULTS

Hippostasin mRNA is expressed preferentially in the normal prostate and weakly in the testis. It was detected in prostate secretory epithelium. Hippostasin protein was localized in the prostate secretory epithelium, and western blotting showed that hippostasin was present in semen. All tested prostate cancer cell lines, including PSA-negative cell lines, expressed hippostasin. Interestingly, all the prostate cancer cell lines expressed only brain-type but not prostate-type hippostasin, while normal prostate and BPH expressed both types of hippostasin

CONCLUSIONS

Our results suggest the possibility that hippostasin may be a useful marker by which prostate cancer and BPH can be distinguished.

Simultaneous quantification of human glandular kallikrein 2 and prostate-specific antigen mRNAs in peripheral blood from prostate cancer patients

We present a multiplexed and internally calibrated quantitative reverse transcription-PCR (QRT-PCR) assay to detect human glandular kallikrein 2 (hK2) and prostate-specific antigen (PSA) transcripts in blood samples from healthy subjects and prostate cancer (PC) patients. The assay detected 50 copies of hK2 and PSA mRNA, and 1 PSA- and 10 hK2-expressing LNCaP cells in the presence of 2.5 x 10(6) PSA- and hK2-negative cells. In PC patients, 20 of 25 and 19 of 25 gave detectable PSA and hK2 mRNAs, respectively. Number of hK2 mRNA copies was significantly higher than that of PSA mRNA copies in patients with biochemically progressive (P = 0.02) PC, and with locally advanced and metastasized (P = 0.004) PC. Patients with rapidly progressive and hormone refractory PC gave detectable hK2 mRNA only in 2 of 8 and PSA mRNA in 3 of 8 patients. Neither PSA nor hK2 mRNAs were detected in 16 healthy subjects. PSA and hK2 discriminated PC patients with biochemically progressive and advanced disease from the controls and from the aggressive distant metastatic disease. The assay provides a reliable quantification of the number of hK2 and PSA mRNA copies, allows to discriminate PC cases from healthy subjects, and offers a tool for further studies on molecular staging of PC.

The new human tissue kallikrein gene family: structure, function, and association to disease

The human tissue kallikrein gene family was, until recently, thought to consist of only three genes. Two of these human kallikreins, prostate-specific antigen and human glandular kallikrein 2, are currently used as valuable biomarkers of prostatic carcinoma. More recently, new kallikrein-like genes have been discovered. It is now clear that the human tissue kallikrein gene family contains at least 15 genes. All genes share important similarities, including mapping at the same chromosomal locus (19q13.4), significant homology at both the nucleotide and protein level, and similar genomic organization. All genes encode for putative serine proteases and most of them are regulated by steroid hormones. Recent data suggest that at least a few of these kallikrein genes are connected to malignancy. In this review, we summarize the recently accumulated knowledge on the human tissue kallikrein gene family, including gene and protein structure, predicted enzymatic activities, tissue expression, hormonal regulation, and alternative splicing. We further describe the reported associations of the human kallikreins with various human diseases and identify future avenues for research.

The expanded human kallikrein (KLK) gene family: genomic organisation, tissue-specific expression and potential functions

The tissue kallikreins are serine proteases encoded by highly conserved multi-gene families. The rodent kallikrein (KLK) families are particularly large, consisting of 13-26 genes clustered in one chromosomal locus. It has been recently recognised that the human KLK gene family is of a similar size (15 genes) with the identification of another 12 related genes (KLK4-KLK15) within and adjacent to the original human KLK locus (KLK1-3) on chromosome 19q13.4. The structural organisation and size of these new genes is similar to that of other KLK genes except for additional exons encoding 5' or 3' untranslated regions. Moreover, many of these genes have multiple mRNA transcripts, a trait not observed with rodent genes. Unlike all other kallikreins, the KLK4-KLK15 encoded proteases are less related (25-44%) and do not contain a conventional kallikrein loop. Clusters of genes exhibit high prostatic (KLK2-4, KLK15) or pancreatic (KLK6-13) expression, suggesting evolutionary conservation of elements conferring tissue specificity. These genes are also expressed, to varying degrees, in a wider range of tissues suggesting a functional involvement of these newer human kallikrein proteases in a diverse range of physiological processes.

KLK12 is a novel serine protease and a new member of the human kallikrein gene family-differential expression in breast cancer

Kallikreins are a subgroup of serine proteases that are involved in the posttranslational processing of polypeptide precursors. Growing evidence suggests that many kallikreins are implicated in carcinogenesis. In rodents, kallikreins are encoded by a large multigene family, but in humans, only three genes have been identified. By using the positional candidate approach, we were able to identify a new kallikrein-like gene, tentatively named KLK12 (for kallikrein gene 12). This new gene maps to chromosome 19q13.3-q13.4, is formed of five coding exons, and shows structural similarity to serine proteases and other known kallikreins. KLK12 is expressed in a variety of tissues including salivary gland, stomach, uterus, lung, thymus, prostate, colon, brain, breast, thyroid, and trachea. We identified three splicing forms of KLK12 that are expressed in many tissues. Our preliminary results indicate that the expression of KLK12 is down-regulated at the mRNA level in breast cancer tissues and is up-regulated by steroid hormones in breast and prostate cancer cell lines. This gene may be involved in the pathogenesis and/or progression of certain cancer types and may find applicability as a novel cancer biomarker.